Ecosyste.ms: Repos

An open API service providing repository metadata for many open source software ecosystems.

GitHub topics: coarse-graining

Repositories

amepproject/amep

The Active Matter Evaluation Package (AMEP) - a Python library for the analysis of particle-based and continuum simulation data of soft and active matter systems

Language: Python - Size: 36.6 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 2 - Forks: 1

marrink-lab/polyply_1.0

Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates

Language: Python - Size: 5.88 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 112 - Forks: 20

GMPavanLab/Swarm-CG

Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization

Language: Python - Size: 32.1 MB - Last synced: 6 days ago - Pushed: almost 3 years ago - Stars: 39 - Forks: 9

cmelab/grits

A toolkit for working with coarse-grain systems

Language: Python - Size: 3.54 MB - Last synced: 20 days ago - Pushed: 21 days ago - Stars: 3 - Forks: 8

marrink-lab/Martini3-small-molecules Fork of ricalessandri/Martini3-small-molecules

Martini 3 small-molecule database

Language: Shell - Size: 27.8 MB - Last synced: 22 days ago - Pushed: 22 days ago - Stars: 4 - Forks: 1

votca/votca

The source of the votca-csg and xtp packages

Language: C++ - Size: 121 MB - Last synced: 4 days ago - Pushed: 5 days ago - Stars: 43 - Forks: 29

ricalessandri/Martini3-small-molecules

Martini 3 small-molecule database

Language: Shell - Size: 27.9 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 50 - Forks: 11

Peppone98/Multiscale_Recoverin

A coarse-grained analysis of the Recoverin protein for the exam of Multiscale Methods

Language: Jupyter Notebook - Size: 247 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

GfellerLab/SuperCell

Coarse-graining of large single-cell RNA-seq data into metacells

Language: R - Size: 77.7 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 54 - Forks: 10

molmod/micmec

MicMec, the first implementation of the micromechanical model, ever.

Language: Python - Size: 20.5 MB - Last synced: 2 months ago - Pushed: 9 months ago - Stars: 6 - Forks: 0

nikhil0165/one_plate_mgrf

Code for solving modified Gaussian renormalized fluctuation theory for a single charged surface

Language: Python - Size: 129 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

SPICA-group/spica-tools

Tools for coarse-grained molecular dynamics simulations using the SPICA force field

Language: Python - Size: 34.1 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 7 - Forks: 2

nikhil0165/two_plates_mgrf

Code for solving modified Gaussian renormalized fluctutation theory for a system of two charged plates

Language: Python - Size: 80.1 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

SIRAHFF/documentation

SIRAH Force Field

Size: 192 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 4 - Forks: 4

gabriele-di-bona/CoarseNet

Collaborative repository to analyse various coarse-graining methods for networks.

Language: Jupyter Notebook - Size: 12.3 MB - Last synced: 10 days ago - Pushed: 7 months ago - Stars: 7 - Forks: 1

mballarin97/DrosophilaNetwork

Analysis from the point of view of network science of the connectome of the drosophila

Language: Jupyter Notebook - Size: 6.68 MB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 1 - Forks: 0

kyonofx/mlcgmd

[TMLR 2023] Simulate time-integrated coarse-grained MD with multi-scale graph neural networks

Language: Python - Size: 47 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 49 - Forks: 5

M4Marvin/Dissertation-MS

Code for analysing coarse grain interaction in Protein-SSDna complexes.

Language: HTML - Size: 12.5 MB - Last synced: 12 months ago - Pushed: 12 months ago - Stars: 0 - Forks: 0

GMPavanLab/SwarmCGM

Optimization tool for calibrating coarse-grained force fields of lipids, relying on the simultaneous usage of reference AA trajectories (bottom-up) and experimental data (top-down)

Language: Python - Size: 482 MB - Last synced: 12 months ago - Pushed: 12 months ago - Stars: 3 - Forks: 0

RSMI-NE/ABsuperdimers

Constructing coarse grained super-dimers on the Ammann-Beenker quasicrystal with RSMI-NE.

Language: Jupyter Notebook - Size: 24.6 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

giorgapost/smith-waterman-algorithm

A C++ implementation of the Smith - Waterman algorithm. The system consists of 3 different implementations: the one is sequential, while the other two parallelize the execution in a coarse and a fine level respectively, with the use of multithreading.

Language: C++ - Size: 4.58 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 2 - Forks: 0